Configuration

The Synapse R Client can be configured either programmatically or by using a configuration file.

Note: The default configuration file does not need to be modified for most use-cases.

Create or edit the .synapseConfig file in your home directory to configure these settings. This file stores configuration options including your Synapse auth token, cache location, multi-threading settings, and storage credentials. See the authentication page for how to set up your credentials in this file.

For a reference showing the available settings and their meanings, see the full annotated example .synapseConfig in the synapseclient GitHub repository.

.synapseConfig sections

[default] and [profile <name>]

Holds Synapse login credentials. [default] is used when no profile is specified; named profiles use [profile <name>] syntax. See the authentication vignette for full details including how to create tokens, select profiles, and use environment variables.

[sftp://hostname]

Credentials for files stored on SFTP servers. Use one section per server; the section name is the full SFTP URL.

Key Description
username Username for the SFTP server.
password Password for the SFTP server. 
[sftp://some.sftp.url.com]
username = sftpuser
password = sftppassword

[https://s3.amazonaws.com/bucket_name]

Credentials for files stored in AWS S3 or S3-compatible storage that Synapse does not manage access for. Use one section per bucket; the section name is the full endpoint URL including the bucket name.

Key Description
profile_name Name of an AWS CLI profile from ~/.aws/credentials. If omitted, the default AWS profile is used. 
[https://s3.amazonaws.com/bucket_name]
profile_name = local_credential_profile_name

For more information on AWS credentials files, see the AWS CLI documentation.

[cache]

Downloaded files are cached to avoid repeat downloads of the same file.

Key Description
location Path to the cache directory. Supports ~ and environment variables. Default: ~/.synapseCache. 
[cache]
location = ~/.synapseCache

[debug]

Note: Debug-level log output is not supported in synapser. The package initializes its underlying Python client with debug=False at load time, so this section has no effect regardless of what is configured here.

[endpoints]

Override the default Synapse production service endpoints. Useful for testing against staging or development environments.

Key Description
repoEndpoint Synapse repository REST API endpoint.
authEndpoint Synapse authentication service endpoint.
fileHandleEndpoint Synapse file service endpoint.
portalEndpoint Synapse web portal URL.

Note: The following are the default endpoints.

[endpoints]
repoEndpoint = https://repo-prod.prod.sagebase.org/repo/v1
authEndpoint = https://auth-prod.prod.sagebase.org/auth/v1
fileHandleEndpoint = https://file-prod.prod.sagebase.org/file/v1
portalEndpoint = https://www.synapse.org/

[transfer]

Settings to configure how Synapse uploads and downloads data.

Key Description
max_threads Number of concurrent threads/connections for file transfers. Applies to AWS S3 transfers (uploads and downloads). Default: min(cpu_count + 4, 128). Maximum: 128. Minimum: 1.
use_boto_sts If true, use AWS STS (Security Token Service) to obtain temporary credentials for S3 transfers instead of using stored AWS credentials directly. Valid values: true or false (case-insensitive). Default: false. 
[transfer]
max_threads = 16
use_boto_sts = false

Note: unlike the Python client, synapser does not currently expose a function to change max_threads programmatically after synLogin() — use the .synapseConfig file shown above to configure this value.